摘要
密码子是生物的重要组成部分,生物体在进化过程中面对复杂多变的环境会偏好使用一部分密码子来提高适应环境的能力,对物种密码子使用模式进行分析,有利于该物种基因的异源表达。本研究使用Codon W软件对薏苡转录组中54275个基因密码子进行分析,统计密码子的相对使用频率(Relative Synonymous Codon Usage,RSCU),确定了薏苡的26个偏好密码子。这些偏好密码子大多以C和U结尾,通过GC 12-GC_(3)和ENC-GC_(3)关联分析及PR 2-plot偏倚分析,发现薏苡密码子除了受到碱基突变的影响外,还受到了自然选择和其他因素的影响。通过分析将薏苡和其他生物的密码子使用频率,发现薏苡密码子使用频率与其他生物存在一定的差异,但与高粱和拟南芥的差异较小,所以拟南芥或许是异源表达的最佳转化供体。
Codons are an important part of organisms.In the process of evolution,organisms prefer to use some codons to improve their ability to adapt to the complex and changeable environment.The analysis of the use pattern of species'codons is conducive to the heterologous expression of genes in the species.In this paper,54275 codons in Coix Lachrymal-jobi L.transcriptome were analyzed using Codon W software,and relative synonymous Codon usage(RSCU)was calculated.Twenty-six preferred codons of Coix Lachrymal-jobi L.were determined.Most of these preferred codons ended in C and U.Correlation analysis of GC 12-GC_(3) and ENC-GC_(3) and bias analysis of PR 2-plot showed that the codon use was influenced by not only base mutation,but also natural selection and other factors.Codon usage frequency of Coix Lachrymal-jobi L and other organisms was analyzed,and codon usage of Coix Lachrymal-jobi L and other organisms was found to be somewhat different from that of other organisms,but less different from sorghum and Arabidopsis thaliana,so Arabidopsis thaliana may be the best transformation donor for allogenic expression.
作者
张重菊
赵懿琛
赵德刚
ZHANG Chongju;ZHAO Yichen;ZHAO Degang(Guizhou Universit,Key Lab of Ministry of Education for Plant Resources Conservation and Germplasm Innovation in Mountainous Region/College of Life Sciences/College of Tea Science,Guiyang 550025,China;Guizhou Academy of Agricultural Sciences,Guiyang 550006,China)
出处
《种子》
北大核心
2022年第4期13-19,共7页
Seed
基金
贵州省农委《薏苡分子育种研究与示范》
贵州省高层次创新人才培养项目(黔科合人才[2016]4003号)。
关键词
薏苡
转录组
偏好密码子
碱基突变
Coix Lachrymal-Jobi L.
transcriptome
preferred codon
base mutation
